I'm sorry, I'm kind of confused. He doesn't warn you about pregnancy, it's a general warning that unexpected things can happen and is using the unexpected thing that happen to himself as just an example. If you're not able to get pregnant the game directly has a character say he didn't mean it like that and doesn't think you're going to get pregnant to make sure it's known. Can you let me know what part made you think he did mean it towards the MC so we can check?
That line can come across that way, but that's why in most cases he says a few lines later that he knows you're not getting pregnant and that's not what he's saying, he's trying to bring up how fast/unexpected things can be. If you're not able to get pregnant, there's also an extra side conversation with Cove after the dad leaves where he also reassures the MC that his dad was being dumb and doesn't mean it that way. It's supposed to be that only if you're able to have kids and decided that you want to have kids that extra conversations about how that was the wrong thing to say might not come up. What's the circumstances of your MC and what is the rest of the conversation until they leave the room? Maybe all the details you have together has a bug and is missing the next parts.
My MC is FTM, going through hormone replacement therapy, and I've honestly never seen any clarification like you're describing so maybe it is a bug. I figure it's because in Step 2 I say I was assigned female at birth.
His dad has never said he knows we're not getting pregnant, and Cove has never reassured me that his dad was just being dumb.